Hi Hendrik, The element msms_pipeline_analysis/msms_run_summary has an attribute base_name to specify the path to the datafile. In case the searched file specified is different from the original data file there is another entry in the element msms_pipeline_analysis/msms_run_summary/search_summary for base_name. As far as I know, there is nothing in the schema that requires these to be unique in the pepXML file. Can you point me to where this constraint is specified in the schema. I checked version 1.8.
-David On Fri, Nov 13, 2009 at 12:31 AM, Eric Deutsch <[email protected]> wrote: > > > Hi Hendrik, I think we need to get an authoritative answer from David on > this one. And he is currently traveling in the Land of the Finns. We will > let/ask him to answer when he is next able. > > Regards, > Eric > > >> From: [email protected] [mailto:spctools- >> [email protected]] On Behalf Of Hendrik Weisser >> >> Hi! >> >> I'm working on the pepXML parser in OpenMS. I've been confronted with >> a type of pepXML file I hadn't seen before, where search results from >> different search engines - but for the same experiment - were >> collected in one file (with one "msms_run_summary" per search engine). >> I've added (maybe prematurely) support for this to the OpenMS parser, >> and then wanted to construct a simple pepXML file for testing >> purposes. >> >> In doing so, I've now come across a constraint in the pepXML schema >> (at least from v1.8 on) that says values of the "base_name" attribute >> (supposed to contain the full path to the searched mzXML file) in the >> "search_summary" element have to be unique within the document. >> What is the rationale behind this constraint? Is it supposed to >> prevent the above case, where different searches of the same >> experiment end up in one file? Why would that be desirable/necessary? >> (Also note that I can construct a valid and parseable pepXML file from >> two different search runs of the same file if I change the path in >> "base_name"...) >> >> In an earlier discussion (http://groups.google.com/group/spctools- >> discuss/msg/7760dcda02877922?hl=en), it was mentioned that >> "base_name"s in "msms_run_summary" elements had to be unique in the >> document - however, as per the schema, that's not true. Also, the >> "base_name" of an "msms_run_summary" is not tied to the "base_name" in >> subordinate "search_summary"s. If there were such a constraint, it >> would be impossible to have more than one "search_summary" under an >> "msms_run_summary" - however, this is allowed in the schema. >> When does it make sense to have different "base_name"s in an >> "msms_run_summary" and its subordinate "search_summary"(s)? Judging >> from the schema documentation and the files I've seen, it seems that >> the values should be the same. On the other hand, why have the >> attribute in both elements then? >> >> All this adds to my confusion about the appropriate use of >> "base_name"... >> >> I would be happy if someone could clear things up for me. >> >> >> Best regards >> >> Hendrik >> >> > > > --~--~---------~--~----~------------~-------~--~----~ > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected] > To unsubscribe from this group, send email to > [email protected] > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en > -~----------~----~----~----~------~----~------~--~--- > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=.
